Data for each isolate
data <- readRDS(here::here("data", "sequencing_log_summary.rds"))
data %>%
datatable(extensions = "Buttons",
# options = list(dom = "Bfrtip",
# buttons = (list(
# "copy", list(
# extend = "collection",
# buttons = c("csv", "excel"),
# text = "Download")))),
rownames = F,
filter = "top",
style = "bootstrap")
Summary all 65 isolates
totals <- data %>% adorn_totals() %>% filter(Sample == "Total")
totals %>% kable() %>% kable_styling(full_width = F)
|
Sample
|
PreMerge
|
Merged
|
Discarded
|
NotAssembled
|
Filtered
|
Chimeric
|
Centroids
|
Centroidswithsupport
|
Aftercontaminantfiltering
|
3D7
|
DD2
|
HB3
|
|
Total
|
6929470
|
6182174
|
0
|
747296
|
1893695
|
348318
|
116224
|
9688
|
2141
|
2
|
6
|
117
|
Flowchart
grViz("digraph flowchart {
# node definitions with substituted label text
node [fontname = Helvetica, shape = rectangle]
tab1 [label = '@@1']
tab2 [label = '@@2']
tab3 [label = '@@3']
tab4 [label = '@@4']
tab5 [label = '@@5']
tab6 [label = '@@6']
# edge definitions with the node IDs
tab1 -> tab2;
tab2 -> tab3;
tab3 -> tab4;
tab4 -> tab5;
tab5 -> tab6
}
[1]: paste0('Raw illumina reads (n = ', totals$PreMerge, ')')
[2]: paste0('Assembled and merged reads (n = ', totals$Merged, ')')
[3]: paste0('Remove chimeras and low quality reads (n = ', totals$Merged-totals$Filtered-totals$Chimeric, ')')
[4]: paste0('Cluster reads at 96% sequence identity (n = ', totals$Centroids, ')')
[5]: paste0('Remove clusters with low support reads (n = ', totals$Centroidswithsupport, ')')
[6]: paste0('Remove non-DBLα sequences, final cleaned DBLα sequences (n = ', totals$Aftercontaminantfiltering, ')')
")